Agreed. I have a development store I closed and would like to delete. I could see the list getting quite long as I spin up new stores for testing purposes. I am pretty surprised that this wasn't a feature from the start. Kind of makes me think that whoever is designing Shopify's new features doesn't really see the whole picture....
This how i close my dev shopify store. First log-in to your development store or whatever. Then Settings > Plan and Permissions > Store Status.
Then hit `Close Store`. After that you you won't be able to view your site. But shopify will allow you to retrieve that close site within 30 days period by logging in to admin. But after that it will be permanently deleted.
Hope this helps!